Bing Liu pittsburgh | Bing Liu bio | Bing Liu: Bing Liu pittsburgh, Bing Liu bio, Bing Liu received Bachelor and PhD in Computer Science under the supervision of Profs P.S. Thiagarajan and David Hsu from National University of Singapore. Previously, Bing Liu have been working with Prof Edmund M. Clarke (Turing Award 2007) as a Postdoctoral Fellow in Department of Computer Science, Carnegie Mellon University, and with Prof Ivet Bahar as a Research Associate in the Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh. Currently, Bing Liu is a Research Assistant Professor in the Department of Computational & Systems Biology, School of Medicine, University of Pittsburgh.
Bing Liu education
- 2006 – 2011, PhD Computational Systems Biology, National University of Singapore
- 2002 – 2006, Bachelor of Computer Science, National University of Singapore
Bing Liu pittsburgh
Bing Liu research area centers on computational systems biology. Liu develop computational modeling, simulation and analysis techniques to study the dynamics of biological systems. As an integral part of my research, Bing Liu collaborate with a number of biologists and clinicians to study a variety of crucial biological processes related to human immunity and cancer. Bing Liu also leverage high-performance computing, formal verification, and machine learning techniques to enable the analysis of multi-scale systems. Furthermore, Bing Liu applying the techniques I have been developing to analyze cyber-physical systems that are ubiquitous in safety-critical applications.
Bing Liu publications
- W Sun, V Tyurin, G Mao, I Shrivastava, B Liu, Y Zhai, S Korolev, A Abramov, P Angelova, I Miller, O Beharier, H Dar, O Kapralov, T Hastings, J Greenamyre, C Chu, I Bahar, Y Sadovsky, H Bayır, Y Tyurina, R He, V Kagan iPLA2G6 Protects Cells against Ferroptosis by Hydrolyzing the Lipid Signal of Death, 15-HpETE-PE: Relevance to Parkinson Disease Pathogenesis, Nature Neuroscience, under review (2020).
PDF - B Liu. A Model Checking-based Analysis Framework for Systems Biology Models, The 57th ACM/IEEE Design Automation Conference (DAC), San Francisco, US (2020). IEEE, pp.1-6
PDF - Q Shi, F Pei, G Silverman, S Pak, D Perlmutter, B Liu, I Bahar. Mechanisms of Action of Autophagy Modulators Dissected by Quantitative Systems Pharmacology Analysis, International Journal of Molecular Sciences, 21(8). 2855 (2020). doi: 10.3390/ijms21082855
PDF - S Thermozier, W Hou, X Zhang, D Shields, R Fisher, H Bayir, V Kagam, J Yu, B Liu, I Bahar, M W Epperly, P Wipf, H Wang, and J S Greenberger. Anti-Ferroptosis Drug Enhances Total Body Irradiation Mitigation by Drugs that Block Apoptosis and Necroptosis, Radiation Research, [Epub ahead of print] (2020). doi: 10.1667/RR15486.1
PDF - O Kapralov, Q Yang, H Dar, Y Tyurina, T Anthonymuthu, R Kim, C St. Croix, K Mikulska-Ruminska, B Liu, I Shrivastava, V Tyurin, H-C Ting, Y Wu, Y Gao, R Domingues, D Stoyanovsky, R Mallampalli, I Bahar, D Gabrilovich, H Bayir, and V Kagan Redox Lipid Reprogramming Commands Susceptibility of Macrophages and Microglia to Ferroptotic Death, Nature Chemical Biology, 16:2780-290 (2020). doi: 10.1038/s41589-019-0462-8
PDF - S Thermozier, X Zhang, W Hou, R Fisher, M W Epperly, B Liu, I Bahar, S Markovina, C Luke, G Silverman, and J S Greenberger. Radioresistance of Serpinb3a-/- Mice and Derived Hematopoietic and Marrow Stromal Cell Lines, Radiation Research, 192(3):267-281 (2019). doi: 10.1667/RR15379.1.
PDF - F Pei, H Li, B Liu, I Bahar. Quantitative Systems Pharmacological Analysis of Drugs of Abuse Reveals the Pleiotropy of Their Targets and the Effector Role of mTORC1, Frontiers in Pharmacology, 10:191 (2019). doi: 10.3389/fphar.2019.00191
PDF - B Liu, B Gyori, P S Thiagarajan. Statistical Model Checking based Analysis of Biological Networks Automated Reasoning for Systems Biology and Medicine, 63-92 (2019). doi: 10.1007/978-3-030-17297-8_3
PDF - J Steinman, M Epperly, Wen Hou, J Willis, H Wang, R Fisher, B Liu, I Bahar, T McCaw, V Kagan, H Bayir, J Yu, P Wipf, S Li, M S Huq, J S Greenberger. Improved Total Body Irradiation Survival by Delivery of Two Radiation Mitigators that Target Distinct Cell Death Pathways, Radiation Research, 189(1):68-83 (2018). doi: 10.1667/RR14787.1
PDF - J S Greenberger, B Liu, I Bahar, H Bayir, and V Kagan. Radiation Disease: Cytokines and the Stages of Apoptosis, Necroptosis, Ferroptosis, Parthanatos, Lysosomal Necrosis, Pyroptosis, and Overlapping Networks, Radiation Biology Methods, Chapter XII (2018).
PDF - J S Greenberger, B Liu, V Kagan, H Bayir, and I Bahar.Radiation Biologic Pathways Intersection and Integration with Other Pathways, Radiation Biology Methods, Chapter XIII (2018).
PDF - B Liu, Z Oltvai, H Bayir, G Silverman, S Pak, D Perlmutter, I Bahar. Quantitative Assessment of Cell Fate Decision between Autophagy and Apoptosis, Nature Scientific Reports, 7:17605 (2017).
PDF - V E Kagan, G Mao, F Qu, J P F Angeli, S Doll, C S Croix, H Dar, B Liu, V A Tyurin, V B Ritov, O A Kapralov, A A Amoscato, J Jiang, T Anthonymuthu, D Mohammadyani, Q Yang, J Klein-Seetharaman, S Watkins, I Bahar, J Greenberger, R Mallampalli, B R Stockwell, Y Y Tyurina, M Conrad, H Bayir. Oxidized Arachidonic and Adrenic PEs Navigate Cells to Ferroptosis, Nature Chemical Biology, 13:81-90 (2017). doi:10.1038/nchembio.2238.
PDF - B Liu, J R Faeder. Parameter Estimation of Rule-based Models Using Statistical Model Checking, IEEE International Conference on Bioinformatics and Biomedicine (BIBM), Shenzhen, China (2016). IEEE, pp. 1458-1464.
PDF - Q Wang, N Miskov-Zivanov, B Liu, J R Faeder, M Lotze, E M Clarke. Formal Modeling and Analysis of Pancreatic Cancer Microenvironment, Computational Methods in Systems Biology (CMSB), Cambridge, UK (2016). Springer, LNCS:9859, pp. 289-305.
PDF - B Liu, Q Liu, S Palaniappan, L Yang, I Bahar, P S Thiagarajan, J L Ding. Innate Immune Memory and Homeostasis May Be Conferred Through crosstalk between TLR3 and TLR7 Pathways, Science Signaling, 9(436) ra70 (2016).
PDF - B Gyori, B Liu, S Paul, R Ramanathan, and P S Thiagarajan. Approximate Probabilistic Verification of Hybrid Systems. Hybrid Systems Biology (HSB), Madrid, Spain (2015). Springer, LNCS:9271, pp. 96-116.
PDF - C Kaya, B Liu, J R Faeder, I Bahar. Unified Model of Synaptic Transmission. Biophysical Journal, 108(2) 155a (2015).
PDF - G F Cooper, I Bahar, M J Becich, P V Benos, J Berg, J U Espino, C Glymour, R C Jacobson, M Kienholz, A V Lee, X Lu, R Scheines, Center for Causal Discovery team. The center for causal discovery of biomedical knowledge from big data Journal of the American Medical Informatics Association, 22(6):1132-1136 (2015).
PDF - B Liu, S Kong, S Gao, P Zuliani and E M Clarke. Towards Personalized Cancer Therapy Using Delta-Reachability Analysis. Hybrid Systems: Computation and Control (HSCC), Seattle, USA (2015). ACM, pp. 227-232.
PDF - B Liu, D Bhatt, Z N Oltvai, J S Greenberger, I Bahar. Significance of p53 Dynamics in Regulating Apoptosis in Response to Ionizing Radiation, and Polypharmacological Strategies. Nature Scientific Reports, 4:6245 (2014).
PDF - B Liu, S Kong, S Gao, P Zuliani and E M Clarke. Parameter Synthesis for Cardiac Cell Hybrid Models Using Delta-Decisions. Computational Methods in Systems Biology (CMSB), Manchester, UK (2014). Springer, LNCS:8859, pp. 99-113.
PDF - H Zhou, S Gao, N N Nguyen, M Fan, J Jin, B Liu, L Zhao, G Xiong, M Tan, S Li, L Wong. Stringent Homology-based Prediction of H. sapiens-M. tuberculosis H37Rv Protein-Protein Interactions. Biology Direct, 9(5):1-52 (2014).
PDF - A Hagiescu, B Liu, R. Ramanathan, S K Palaniappan, Z Cui, B Chattopadhyay, W F Wong, P S Thiagarajan. GPU Code Generation for ODE-Based Applications with Phased Shared-data Access Patterns. ACM Transactions on Architecture and Code Optimization, 10(4):551-5519 (2013).
PDF - S Palaniappan, B Gyori, B Liu, D Hsu, P S Thiagarajan and E M Clarke. Statistical Model Checking Based Calibration and Analysis of Bio-pathway Models. Computational Methods in Systems Biology (CMSB), Klosterneuburg, Austria (2013). Springer, LNCS:8130, pp 120-134.
PDF - B Liu, S Kong, S Gao, and E M Clarke. Parameter Identification Using Delta-Decisions for Biological Hybrid Systems. CMU SCS Technical Report, CMU-CS-13-136 (2013).
PDF - B Liu, A Hagiescu, S K Palaniappan, B Chattopadhyay, Z Cui, W F Wong, P S Thiagarajan. Approximate Probabilistic Analysis of Biopathway Dynamics. Bioinformatics, 28(11):1508-1516 (2012).
PDF - S K Palaniappan, S Akshay, B Liu, B Genest, P S Thiagarajan. A Hybrid Factored Frontier Algorithm for Dynamic Bayesian Networks with a Biopathways Application. IEEE/ACM Transactions on Computational Biology and Bioinformatics, 9(5):1352-1365 (2012).
PDF - B Liu, P S Thiagarajan. Modeling and Analysis of Biopathways Dynamics. Journal of Bioinformatics and Computational Biology, 10(4):1231001 (2012).
PDF - B Liu, J Zhang, P Y Tan, D Hsu, A M Blom, B Leong, S Sethi, B Ho, J L Ding, P S Thiagarajan. A Computational and Experimental Study of the Regulatory Mechanisms of the Complement System. PLoS Computational Biology, 7(1):e1001059 (2011).
PDF News@NGS Website - B Liu, D Hsu, P S Thiagarajan. Probabilistic Approximations of ODEs based Bio-Pathway Dynamics. Theoretical Computer Science, 412(21):2188-2206 (2011).
PDF - B Liu, P S Thiagarajan, D Hsu. Probabilistic Approximations of Signaling Pathway Dynamics. Computational Methods in Systems Biology (CMSB) , Bologna, Italy (2009). Springer, LNCS:5688, pp. 251-265.
PDF - B Liu. Statistical analysis of partially calibrated bio-pathway models. HPC E-newsletter Issue No. 24. (HPC Challenge 2009 Winning Project) (2009).
PDF - T Zhu, P Korshunov, B Liu, W T Ooi. Plasma: A Scripting Language for Processing Media Streams. ACM/SPIE Multimedia Computing and Networking (MMCN), San Jose, US (2007). Proceedings of SPIE:6504, pp. 65040Q.
PDF - B Liu, W T Ooi. SLIME: A Tool for Composing Live and Stored Media. In Proc. of the 11th NUROP Congress, Singapore (2006).
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Bing Liu talks
- TLR Pathways Crosstalk Confers Innate Immune Memory. Systems Immunology Research Forum, March 2019, Pittsburgh, US.
- Systems Biology, Artificial Intelligence, and Better Life. Fudan-Guanghua International Forum for Young Scholars, December 2018, Shanghai, China
- Deciphering Complex Signaling Networks in Asthma. The 6th International Conference on Mathematical Biology (ICMB), June 2018, Beijing, China.
- Systems-level Insights into Cell Death from Quantitative Modeling. CMCR Seminar, October 2017, Pittsburgh, US.
- Decipher Biological Machinery . Sun Yat-sen University University, June 2017, Zhuhai, China.
- Model Checking, Systems Biology, and Better Therapeutics. Fudan University, December 2016, Shanghai, China.
- Model Checking, Systems Biology, and Better Therapeutics. Soochow University, December 2016, Suzhou, China.
- Parameter Estimation of Rule-based Models Using Statistical Model Checking. IEEE International Conference on Bioinformatics and Biomedicine (BIBM),, December 2016, Shenzhen, China.
- Systems-level Insights into Cellular Regulation from Quantitative Modeling. National Institute of Mental Health, August 2016, Washington DC, US.
- Model Checking Biology Systems. UPPDA P2P, October 2015, Pittsburgh, US.
- Towards Prostate Personalized Cancer Therapy Using Delta-Reachability Analysis. The 18th ACM International Conference on Hybrid Systems: Computation and Control (HSCC), April 2015, Seattle, US.
- Computational Modeling of the Crosstalk Between Autophagy and Apoptosis. Biophysical Theory Club, March 2015, Pittsburgh, US.
- Mathematical Modeling of TLR3-TLR7 Signaling Crosstalk. CSB-Squared, December 2014, Pittsburgh, US.
- Parameter Identification using Model Checking for Systems Biology. Clarke Symposium, September 2014, Pittsburgh, US.
- Parameter Identification using Delta-Decisions for Hybrid Systems in Biology. CMACS/AVACS Workshop, November 2013, Pittsburgh, US.
- Approximation and Verification Techniques for Biology Pathway Modeling. National Heart, Lung, and Blood Institute, NIH, November 2013, Washington DC, US.
- Probabilistic Approximation Techniques for Biopathway Modeling. CMACS Seminar, November 2012, Pittsburgh, US.
- Probabilistic Approximation Techniques for Biopathway Modeling. Biophysical Theory Club, October 2012, Pittsburgh, US.
- Probabilistic Approximation Techniques for Biopathway Modeling. INRIA Contraintes Seminar, April 2012, Paris, France.
- Probabilistic Approximation Techniques for Biopathway Modeling. Global-COE Workshop on Engineering/Information Science for Integrated Life Science and Predictive Medicine, February 2012, Singapore.
- A Platform-aware GPU Realization of A Systems Biology Application. The 3nd NUS-U.Tokyo Joint Workshop on Computational Systems Biology, April 2011, Singapore.
- Computational and Experimental Study of Complement System. The 2nd NUS-U.Tokyo Joint Workshop on Computational Systems Biology, February 2010, Tokyo, Japan.
- Probabilistic Approximations of ODE-based Bio-Pathway Dynamics. Applied and Computational Math Seminar, February 2010, Singapore.
- Statistical Analysis of Partially Calibrated Bio-pathways Models. High Performance Computing Challenge Ceremony, November 2009, Singapore.
- Probabilistic Approximations of Signaling Pathway Dynamics. the 7th International Conference on Computational Methods in Systems Biology (CMSB), September 2009, Bologna, Italy.
- Probabilistic Approximations of Signaling Pathway Dynamics. The 1st NGS Student Symposium, February 2009, Singapore.
- Stochastic Approximations of Signaling Pathway Dynamics. The 1st NUS-U.Tokyo Joint Workshop on Computational Systems Biology, September 2008, Singapore.